Simultaneous removal of aliphatic and aromatic crude oil hydrocarbons by Pantoea agglomerans isolated from petroleum-contaminated soil in the west of Iran.

Hydrocarbons are considered as one of the most common and harmful environmental pollutants affecting human health and the environment. Bioremediation as an environmentally friendly, highly efficient, and cost-effective method in remediating oil-contaminated environments has been interesting in recent decades. In this study, hydrocarbon degrader bacterial strains were isolated from the highly petroleum-contaminated soils in the Dehloran oil field in the west of Iran. Out of 37 isolates, 15 can grow on M9 agar medium that contains 1.5 g L-1 of crude oil as the sole carbon source. The morphological, biochemical, and 16SrRNA sequencing analyses were performed for the isolates. The choosing of the isolates as the hydrocarbon degrader was examined by evaluating the efficacy of their crude oil removal at a concentration of 10 g L-1 in an aqueous medium. The results showed that five isolates belonging to Pseudomonas sp., Pseudomonas oryzihabitans, Roseomonas aestuarii, Pantoea agglomerans, and Arthrobacter sp. had a hyper hydrocarbon-degrading activity and they could remove more than 85% of the total petroleum hydrocarbon (TPH) after 96 h. The highest TPH removal of about 95.75% and biodegradation rate of 0.0997 g L-1 h-1 was observed for P. agglomerans. The gas chromatography-mass spectroscopy (GC-MS) analysis was performed during the biodegradation process by P. agglomerans to detect the degradation intermediates and final products. The results confirmed the presence of intermediates such as alcohols and fatty acids in the terminal oxidation pathway of alkanes in this biodegradation process. A promising P. agglomerans NB391 strain can remove aliphatic and aromatic hydrocarbons simultaneously.

Potential of indigenous bacteria driven U(VI) reduction under relevant deep geological repository (DGR) conditions.

Understanding the biogeochemical U redox processes is crucial for controlling U mobility and toxicity under conditions relevant to deep geological repositories (DGRs). In this study, we examined the microbial reduction of aqueous hexavalent uranium U(VI) [U(VI)aq] by indigenous bacteria in U-contaminated groundwater. Three indigenous bacteria obtained from granitic groundwater at depths of 44-60 m (S1), 92-116 m (S2), and 234-244 m (S3) were used in U(VI)aq bioreduction experiments. The concentration of U(VI)aq was monitored to evaluate its removal efficiency for 24 weeks under anaerobic conditions with the addition of 20 mM sodium acetate. During the anaerobic reaction, U(VI)aq was precipitated in the form of U(IV)-silicate with a particle size >100 nm. The final U(VI)aq removal efficiencies were 37.7%, 43.1%, and 57.8% in S1, S2, and S3 sample, respectively. Incomplete U(VI)aq removal was attributed to the presence of a thermodynamically stable calcium uranyl carbonate complex in the U-contaminated groundwater. High-throughput 16S rRNA gene sequencing analysis revealed the differences in indigenous bacterial communities in response to the depth, which affected to the U(VI)aq removal efficiency. Pseudomonas peli was found to be a common bacterium related to U(VI)aq bioreduction in S1 and S2 samples, while two SRB species, Thermodesulfovibrio yellowstonii and Desulfatirhabdium butyrativorans, played key roles in the bioreduction of U(VI)aq in S3 sample. These results indicate that remediation of U(VI)aq is possible by stimulating the activity of indigenous bacteria in the DGR environment.

Hydrocarbons removal and microbial community succession in petroleum-contaminated soil under hydrogen peroxide treatment.

Chemical oxidation as a pretreatment step coupled with bioremediation for petroleum-contaminated soil may pose serious impacts on indigenous microorganisms and the available nutrients. Petroleum-contaminated soil were treated by hydrogen peroxide (H2O2) at initial concentrations of 105 mM (HH), 21 mM (HL), and 105 mM in three equal amounts (HT) without adding any external catalyst. The contents of total petroleum hydrocarbons (TPH) and dissolved nutrients (total organic compounds, nitrogen, and phosphate), and the indigenous bacteria community succession (analyzed by high-throughput sequencing of 16S rDNA) were investigated over 50 days. Compared to the control treatment without H2O2 addition, H2O2 treatments for the petroleum-contaminated soil significantly promoted the TPH removal especially in the first 4 days and impacted the contents of dissolved nutrients. Both of chemical oxidation and nutrients contributed to microbial community structure changes in alpha diversity. Although the soil microbial community structure had undergone significant changes after different chemical oxidation pretreatments, Firmicutes, Proteobacteria, Gemmatimonadetes, and Actinobacteria were the main bacterial phyla. Compared with adding H2O2 at one time, H2O2 added in stepwise was beneficial to indigenous bacterial diversity recovery and TPH removal. H2O2 oxidation treatments showed a great influence on the microbial community structures in the start-up stage, while recovery time rather than the oxidation treatments presented greater effects on the composition of the microbial community structure with the incubation time extended. Therefore, adding H2O2 as pretreatment for petroleum-contaminated soil showed little effect on the structure of soil indigenous microbial community from a long-term scale, and was conducive to the continuous removal of TPH by indigenous microorganisms.

Isolation, selection and evaluation of Bacillus spp. as potential multi-mode probiotics for poultry.

Bacillus based probiotics are becoming relevant as alternatives to antibiotics used in poultry production and in other animal husbandry. This study describes the isolation of 48 Bacillus spp. candidates, from chickens and chicken environments, for use as potential probiotics in poultry production. These isolates, plus a further 18, were tested in a comprehensive in vitro screening regime that was specifically designed to select the best isolates that satisfied multiple modes of action desirable for commercial poultry probiotics. This screening programme involved the evaluation of the ability of the isolates to survive and grow in the limiting conditions of the chicken gastrointestinal tract. Only 11 of the isolates fulfilled these criteria; hence, they were further evaluated for the ability to adhere to epithelial cells, produce extracellular enzymes, and to demonstrate antagonistic activity against selected pathogens of significant importance in poultry production. Of these, a total of 6 isolates were selected, due to their all-round probiotic capability. Identification by 16S RNA sequencing confirmed these isolates as B. subtilis and B. velezensis, identities which are generally regarded as safe. The Bacillus isolates reported in our study exhibit strong all-inclusive probiotic effects and can potentially be formulated as a probiotic preparation for poultry production.

Rapid degradation of long-chain crude oil in soil by indigenous bacteria using fermented food waste supernatant.

The objective of this study is to explore how to stimulate soil indigenous bacteria for the degradation of long-chain crude oil by adding fermented food waste supernatant (FS). Four concentrations of FS (0 mL, 0.1 mL, 1 mL, and 3 mL) were added to two oil-contaminated soils S1 and S2 for 30 days of bioremediation experiments. The results showed that the biodegradation of long-chain alkanes (C29 - C24) could reach up to 1756 mg/kg (49.3%, S1) and 3937 mg/kg (43.9%, S2), which were 3.1 and 3.2 times that of the non-nutrient system. In addition, the logarithmic growth rate of the indigenous hydrocarbon degraders (IHD) reached 41.5%. The long-chain crude oil can be rapidly degraded by indigenous bacteria with FS added in a short time. The glucose and acetic acid accelerated the consumption of ammonia nitrogen (NH4+-N) in the prophase of bioremediation and the molar ratio of consumed carbon (contained in glucose and acetic acid) to consumed NH4+-N (C/N) was high by adding FS. Thus, the IHD can multiply rapidly. The analysis of microbial diversity revealed that the IHD (genera Acinetobacter and Aquabacterium) became the dominant bacteria. Long-chain alkanes became the main carbon sources for IHD after 14 days in soil S1 and 16 days in soil S2. Thus, the rapid biodegradation of long-chain crude oil was achieved. The genus Aquabacterium which was uncultivable on crude oil medium became the dominant bacteria. This study provides an environment-friendly and sustainable remediation technology for bioremediation of oil-contaminated soils.

Biomineralisation performance of bacteria isolated from a landfill in China.

We report an investigation of microbially induced carbonate precipitation by seven indigenous bacteria isolated from a landfill in China. Bacterial strains were cultured in a medium supplemented with 25 mmol/L calcium chloride and 333 mmol/L urea. The experiments were carried out at 30 °C for 7 days with agitation by a shaking table at 130 r/min. Scanning electron microscopic and X-ray diffraction analyses showed variations in calcium carbonate polymorphs and mineral composition induced by all bacterial strains. The amount of carbonate precipitation was quantified by titration. The amount of carbonate precipitated in the medium varied among isolates, with the lowest being Bacillus aerius rawirorabr15 (LC092833) precipitating around 1.5 times more carbonate per unit volume than the abiotic (blank) solution. Pseudomonas nitroreducens szh_asesj15 (LC090854) was found to be the most efficient, precipitating 3.2 times more carbonate than the abiotic solution. Our results indicate that bacterial carbonate precipitation occurred through ureolysis and suggest that variations in carbonate crystal polymorphs and rates of precipitation were driven by strain-specific differences in urease expression and response to the alkaline environment. These results and the method applied provide benchmarking and screening data for assessing the bioremediation potential of indigenous bacteria for containment of contaminants in landfills.

Biodegradation of marine oil spill residues using aboriginal bacterial consortium based on Penglai 19-3 oil spill accident, China.

Bioremediation, mainly by indigenous bacteria, has been regarded as an effective way to deal with the petroleum pollution after an oil spill accident. The biodegradation of crude oil by microorganisms co-incubated from sediments collected from the Penglai 19-3 oil platform, Bohai Sea, China, was examined. The relative susceptibility of the isomers of alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophene to biodegradation was also discussed. The results showed that the relative degradation values of total petroleum hydrocarbon (TPH) are 43.56% and 51.29% for sediments with untreated microcosms (S-BR1) and surfactant-treated microcosms (S-BR2), respectively. TPH biodegradation results showed an obvious decrease in saturates (biodegradation rate: 67.85-77.29%) and a slight decrease in aromatics (biodegradation rate: 47.13-57.21%), while no significant difference of resins and asphaltenes was detected. The biodegradation efficiency of alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophene for S-BR1 and S-BR2 samples reaches 1.28-84.43% and 42.56-86.67%, respectively. The efficiency of crude oil degradation in sediment with surfactant-treated microcosms cultures added Tween 20, was higher than that in sediment with untreated microcosms. The biodegradation and selective depletion is not only controlled by thermodynamics but also related to the stereochemical structure of individual isomer compounds. Information on the biodegradation of oil spill residues by the bacterial community revealed in this study will be useful in developing strategies for bioremediation of crude oil dispersed in the marine ecosystem.

Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea.

The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons. Three phyla (Proteobacteria, Firmicutes, and Bacteroidetes) accounted for approximately ≥93.0% of the total phyla based on metagenomic analysis. Proteobacteria was the dominant phylum in Sinduri beach sediments. Cultivable bacteria were isolated from PAH-enriched cultures, and bacterial diversity was investigated through performing culture characterization followed by molecular biology methods. Sixty-seven isolates were obtained, comprising representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, and Bacteroidetes. PAH catabolism genes, such as naphthalene dioxygenase (NDO) and aromatic ring hydroxylating dioxygenase (ARHDO), were used as genetic markers to assess biodegradation of PAHs in the cultivable bacteria. The ability to degrade PAHs was demonstrated by monitoring the removal of PAHs using a gas chromatography mass spectrometer. Overall, various PAH-degrading bacteria were widely present in Sinduri beach sediments and generally reflected the restored microbial community. Among them, Cobetia marina, Rhodococcus soli, and Pseudoalteromonas agarivorans were found to be significant in degradation of PAHs. This large collection of PAH-degrading strains represents a valuable resource for studies investigating mechanisms of PAH degradation and bioremediation in oil contaminated coastal environment, elsewhere.

Effect of Fenton pre-oxidation on mobilization of nutrients and efficient subsequent bioremediation of crude oil-contaminated soil.

Fenton pre-oxidation and a subsequent bioremediation phase of 80 days were used to investigate the importance of matching concentration of residual indigenous bacteria and nutrient levels on subsequent bioremediation of crude oil. Experiments were performed using either high (>107.7 ± 0.2 CFU/g soil) or low (<105.9 ± 0.1 CFU/g soil) concentrations of bacteria and three different nutrient levels: enough (C/N > 9.8), moderate (C/N:5-9.8), and lacking nutrient level (C/N < 5) conditions. Weak Fenton pre-oxidation (225 mM H2O2 and 2.9 mM Fe2+) resulted in highly matching between nutrient level and the population of residual indigenous bacteria. Up to 53% of total petroleum hydrocarbon (TPH) and 58% of main hydrocarbon (C15C25, during the first 10 days) were removed from the soil. Under matching conditions, the activity of indigenous bacteria and nutrient mobilization were enhanced, promoting the bioremediation of crude oil. In addition, the biodegradation of long chain molecules (C26C30) required a high level of NH4+-N.

Impact of chemical oxidation on indigenous bacteria and mobilization of nutrients and subsequent bioremediation of crude oil-contaminated soil.

Fenton pre-oxidation provides nutrients to promote bioremediation. However, the effects of the indigenous bacteria that remain following Fenton oxidation on nutrient mobilization and subsequent bioremediation remain unclear. Experiments were performed with inoculation with native bacteria and foreign bacteria or without inoculation after four regimens of stepwise pre-oxidations. The effects of the indigenous bacteria remaining after stepwise oxidation on nutrient mobilization and subsequent bioremediation over 80 days were investigated. After stepwise Fenton pre-oxidation at a low H2O2 concentration (225×4), the remaining indigenous bacterial populations reached their peak (4.8±0.17×106CFU/g), the nutrients were mobilized rapidly, and the subsequent bioremediation of crude oil was improved (biodegradation efficiency of 35%). However, after stepwise Fenton pre-oxidation at a high H2O2 concentration (450×4), only 3.6±0.16×103CFU/g of indigenous bacteria remained, and the indigenous bacteria that degrade C15-C30 alkanes were inhibited. The nutrient mobilization was then highly limited, and only 19% of total petroleum hydrocarbon was degraded. Furthermore, the recovery period after the low H2O2 concentration stepwise Fenton pre-oxidation (225×4) was less than 20 days, which was 20-30 days shorter than with the other pre-oxidation treatments. Therefore, stepwise Fenton pre-oxidation at a low H2O2 concentration protects indigenous bacterial populations and improves the nutrient mobilization and subsequent bioremediation.

Treatment of high-salinity chemical wastewater by indigenous bacteria--bioaugmented contact oxidation.

A 90 m(3) biological contact oxidation system in chemical factory was bioaugmented with three strains of indigenous salt-tolerant bacteria. These three strains were screened from contaminative soil in situ. Their activity of growth and degradation was investigated with lab-scale experiments. Their salt-tolerant mechanism was confirmed to be compatible-solutes strategy for moderately halophilic bacteria, with amino acid and betaine playing important roles. The running conditions of the system were recorded for 150 days. The indigenous bacteria had such high suitability that the reactor got steady rapidly and the removal of COD maintained above 90%. It was introduced that biofilm fragments in sedimentation tank were inversely flowed to each reaction tank, and quantitative PCR demonstrated that this process could successfully maintain the bacterial abundance in the reaction tanks. In addition, the T-RFLP revealed that bioaugmented strains dominated over others in the biofilm.